Robert VanBuren of the Danforth Plant Science Center and winner of the 2014 SMRT Grant Program presents a de novo assembly of the Oro grass genome (Oropetium thomaeum). The reference genome will aid scientist studying drought tolerance in common crop species, especially cereals, though comparative genomics to understand potential key genetic underpinnings for this “resurrection” trait. Initial comparative results to Brachypodium and maize are presented, as well as secondary analysis to identify key metabolic traits.
In this webinar, the presenters describe a targeted sequencing workflow that combines Roche NimbleGen’s SeqCap EZ enrichment technology with PacBio’ SMRT Sequencing to provide a more comprehensive view of variants and haplotype information over multi-kilobase, contiguous regions. They demonstrate that 6 kb fragments can also be utilized to enrich for long fragments that extend beyond the targeted capture site and well into (and often across) the adjacent intronic regions. When combined with SMRT Sequencing, multi-kilobase genomic regions can be phased and variants, including complex structural variants, can be detected in exons, introns and intergenic regions.
Alan Archibald compares two new de novo PacBio pig genome assemblies to a previously released draft genome, finding significant improvement that could be important for breeding programs. In one example, he shows chromosome 1, which was split into more than 9,000 contigs in the draft genome, is now represented in just 10 contigs.
PacBio’s Jenny Gu and Christina Tran from Experiment talk about the use of alternative funding sources to support SMRT Sequencing projects. The Genome Galaxy Initiative is a new program from PacBio that helps scientists launch their long-read sequencing projects on Experiment’s crowdfunding platform. Experiment has raised more than $5 million to fund hundreds of scientific projects since it kicked off in 2012.
Michiel van Eijk of KeyGene shared a de novo PacBio assembly of tetraploid cotton. The genome assembly was further enhanced and annotated using Iso-Seq data collected from cotton root, leaf, and stem tissues. The data, full-length cDNA transcripts, captured alternative splicing diversity across these tissue types, allowing for isoform differentiation.
Susan Strickler of the Boyce Thompson Institute presented strategies for assembling the genome of Arabica coffee, an allotetraploid with a genome size of approximately 1.3 Gb. A de novo PacBio assembly was constructed and presented. The new high-quality reference will be used to guide assemblies of the diploid ancestors of Arabica coffee and re-sequencing data for a set of C. arabica accessions to more fully characterize the genetic diversity of this crop species that is highly susceptible to climate change.
In this webinar, Elizabeth Tseng from PacBio demonstrates how to run the Iso-Seq bioinformatics software pipeline that is part of PacBio’s SMRTAnalysis software suite. Both the web portal interface (SMRT Portal) and the command line version will be introduced. In addition, she reviews the community version of Iso-Seq (pbtranscript-tofu) and other community tools to perform additional analyses.
In this webinar, Tyson Clark from PacBio discusses the recent Iso-Seq template preparation protocol updates for creating full-length cDNAs and discusses considerations for experimental design.
Tim Smith from the USDA’s Agricultural Research Service talks about using long-read sequencing to redo assemblies for cattle, swine, sheep, and goat. Long-read assemblies correct misassemblies and other problems from older genome projects. Smith says SMRT Sequencing has also made possible isoform sequencing as well as microbiome characterization.
Doreen Ware introduces her team’s new assembly of maize, built with PacBio long-read sequencing and genome maps from BioNano Genomics. With a contig N50 of nearly 10 Mb and more complete information than any previous assembly, Ware says, “This is just an amazing time to be a plant scientist.” Her presentation includes a number of highlights from the new assembly, which may help crop improvement efforts for maize.
Oliver Ryder speaks about efforts to rescue the Hawaiian crow, a bird that has been extinct in the wild since 2002, and reintroduce it to its native habitat. Critical to this work is a new SMRT Sequencing reference genome assembly, which Ryder says is already one of the best avian assemblies out there. The resource may help deal with challenges like inbreeding and disease susceptibility.
Ho Yung Shwen presented this talk about a new genome assembly of Chenopodium quinoa, the native South American plant known for its ability to grow in harsh environments. He used SMRT Sequencing and other tools to characterize the organism’s allotetraploid genome and to infer new information about the plant’s unknown diploid ancestors
Evan Eichler, Howard Hughes Medical Investigator from the University of Washington discusses his use of the PacBio system to study difficult-to-sequence regions of the human and chimp genomes. Eichler has identified a number of rapidly evolving hot spots in the human genome that are associated with disease. These regions are quite long and have extremely repetitive DNA sequence, making them difficult to elucidate with short-read sequencing and very expensive to interrogate with Sanger sequencing. Eichler’s goal is to fill in the missing regions of the human genome reference, many of which contain segmental duplications.
Swati Ranade from PacBio presents recent efforts to look at challenging regions of the human genome using SMRT Sequencing. She highlights a study just published that fully sequences a particular mucin gene for the first time, as well as work on KIR haplotypes in humans and other primates.
In this presentation, Greg Harhay from the USDA offers data on pathogens involved in bovine respiratory disease complex, known as “shipping fever.” His team used PacBio sequencing to analyze several isolates from two different pathogens, looking at their DNA sequence and methylation patterns.